📝 ✏️ updating usage documentation

small typo in Run.sh mismatch between branches

README.md

@@ -10,6 +10,8 @@ Repository for the [UNRESP](https://vumo.cloud/) Forecasting System:
 
 An automated forecasting system has been created that uses the [CALPUFF](http://www.src.com/) dispersion model to predict S02 and S04 concentrations around the Masaya volcano. This is based on the current forecasting system implemented by IMO, but with modifications and improvements.
 
+This work is displayed [here]([~earunres](https://homepages.see.leeds.ac.uk/~earunres))
+
 ## Description ##
 
 The repository hosts the scripts required to run the CALPUFF dispersion model to predict SO2 concentrations around the Masaya volcano forecasting for 48 hours using NAM data. The hourly output is plotted in individual png files and collated into a mp4 movie.
@@ -26,6 +28,15 @@ python 3**
 
 Aimed at running on the Leeds Linux systems
 
+```bash
+./Run.sh
+optional arguments
+-d Date YYYYMMDD, defaults to  
+-n specify home directory, defaults to ~earunres
+-h help prints Usage statement and exits
+```
+This set up defaults to production behaviour to run as a chronjob displaying at [~earunres](https://homepages.see.leeds.ac.uk/~earunres/UNRESP_VIZ/index.html)
+
 * In Run.sh various parameters can be set:
   1. `res` to alter the resolution between 100 - 1000 m
   2. `runVis=True` Enable visualization  creating static and movie visualisations of the CALPUFF model output via a python script (generateMaps.py) and the Linux tool 'ffmpeg', respectively.
@@ -35,13 +46,13 @@ Aimed at running on the Leeds Linux systems
   6. `run3DDAT=true` - Downloads the required met (NAM) data and runs a python script (Create3DDAT.py) to extract the required data into a file appropriate for input to CALMET.
   7. `runCALMET=true` - The 3-D diagnostic meteorological model part of the CALPUFF system
   8. `runCALPUFF=true` - The main dispersion model part of the CALPUFF system
-* To forecast for the current day:
+* To forecast for the current day default visualization home to ~earunres (production):
   ```bash
   ./Run.sh
   ```
 * To forecast for a specific day:
   ```bash
-  ./Run.sh YYYYMMDD
+  ./Run.sh -d YYYYMMDD
   ```
   Note, however, that the external met (NAM) data that the script will try to download is only accessible for around 10 days after the original date before it is removed from the ftp site.
 * Chronjobs: 2 chronjobs are required
@@ -80,6 +91,17 @@ The directory structure of the repository is as follows:
 
 <hr>
 
+## Version information
+
+
+<!--- release table --->
+|  Version            | Release          |
+|---------------------|------------------|
+| **UoL original**  | [![GitHubrelease](https://img.shields.io/badge/release-v.1.0-blue.svg)](https://github.com/cemac/DECAF_workflow/releases/tag/v1.0)|
+| **Viz update**    |  [![GitHubrelease](https://img.shields.io/badge/release-v.2.0.2-blue.svg)](https://github.com/cemac/UNRESPForcastingSystem/releases/tag/v2.0.2) |
+| **SO4** |  *coming soon*     |
+<!--- table --->
+
 ## Acknowledgements ##
 
 *Comming soon*

Run.sh

@@ -6,28 +6,14 @@
 set -e #stop at first error
 module load intel/17.0.0
 module load python2 python-libs
-# Defaults
-rundate=$(date +%Y%m%d)
-vizhome=~earunres
-
-print_usage() {
-  echo "Usage:
- -d date YMD defaults to today
- -n name of viz defaults to ~earunres"
-}
-
-while getopts 'dn:hv' flag; do
-  case "${flag}" in
-    d) rundate="${OPTARG}" ;;
-    n) vizhome="${OPTARG}" ;;
-    v) verbose=true ;;
-    h) print_usage
-       exit 1 ;;
-    *) print_usage
-       exit 1 ;;
-  esac
-done
 
+#Read in command line arguments and set subsequent variables
+if [ $# -eq 0 ]
+  then
+    rundate=$(date +%Y%m%d)
+else
+  rundate=$1
+fi
 prevdate=$(date -d "$rundate - 1 day" +%Y%m%d)
 middate=$(date -d "$rundate + 1 day" +%Y%m%d)
 enddate=$(date -d "$rundate + 2 days" +%Y%m%d)
@@ -49,15 +35,16 @@ run3DDAT=true
 runCALMET=true
 runCALPUFF=true
 runVIS=true
-runffmpeg=false
+runffmepg=false
+
 #Set other parameters
 res=1000 #Resolution (m) of intended CALPUFF grid. Should be an integer that is > 100 and < 1000
 let NX=90000/$res+1
 let NY=54000/$res+1
 DGRIDKM=$(echo "scale=3; $res/1000" | bc)
 let MESHGLAZ=1000/$res+1
 # VISUALISATION  PATH
-VIZPATH=$vizhome/public_html/UNRESP_VIZ/
+VIZPATH=~/public_html/UNRESP_VIZ/
 cwd=$(pwd)
 
 echo "### RUNNING FORECAST SYSTEM FOR DATE "${rundate}" ###"
@@ -191,7 +178,7 @@ if [ "$run3DDAT" = true ]; then
 	#Entire GRIB file:
 	#wget http://www.ftp.ncep.noaa.gov/data/nccf/com/nam/prod/nam.${rundate}/nam.t00z.afwaca${hour}.tm00.grib2
 	#Subset of GRIB file using GRIB filter (http://nomads.ncep.noaa.gov/cgi-bin/filter_nam_crb.pl):
-	curl "https://nomads.ncep.noaa.gov/cgi-bin/filter_nam_crb.pl?file=nam.t00z.afwaca"${hour}".tm00.grib2&"\
+	curl "http://nomads.ncep.noaa.gov/cgi-bin/filter_nam_crb.pl?file=nam.t00z.afwaca"${hour}".tm00.grib2&"\
 "lev_1000_mb=on&lev_100_mb=on&lev_10_mb=on&lev_150_mb=on&lev_200_mb=on&lev_20_mb=on&lev_250_mb=on&"\
 "lev_2_mb=on&lev_300_mb=on&lev_30_mb=on&lev_400_mb=on&lev_500_mb=on&lev_50_mb=on&lev_5_mb=on&"\
 "lev_600_mb=on&lev_700_mb=on&lev_75_mb=on&lev_7_mb=on&lev_800_mb=on&lev_850_mb=on&lev_900_mb=on&"\
@@ -339,17 +326,15 @@ if [ "$runVIS" = true ]; then
   ./generateMaps.py ${rundate}
   cd ..
   cd vis/${rundate}
-  if [ "$runffmpeg" = true]; then
-  echo "Running ffmpeg"
-  ffmpeg -f image2 -r 4 -i static_concrec0100%02d.png -vcodec mpeg4 -y -s 7680x4320 movie_${rundate}.mp4
+  if [ "$runffmepg" = true ]; then
+    ffmpeg -f image2 -r 4 -i static_concrec0100%02d.png -vcodec mpeg4 -y -s 7680x4320 movie_${rundate}.mp4
   fi
   cd ../..
   echo " ---> FINISHED ###"
 
-  echo "Adding latest VISUALISATION to website at "$VIZPATH
+  echo "Adding latest VISUALISATION to website"
 
   cd vis/${rundate}
-  echo "Reformatting png to jpg"
   mogrify -format jpg *.png
   rm -f *.png
   setfacl -m other:r-x *.jpg *.html